Let me go through a breakdown of each character...
Mouri Ran - Karate Black Belt and captain of the HS Karate team. Is shown to be proficient at many kicks and physically very strong. Easily defeated when scared or unprepared. In competition she is probably very effective, but not so much in the real world.
Mouri Kogorou - [likely] A Judo black belt. Sucked in competition, was great in practice. Also a former police detective, meaning he dealt with criminals on a regular basis. Has been shown to be proficient in a pinch, and has great reaction. He is a strong contender.
Kazuha Toyama - Proficient in Aikido. The softest of the martial arts of the characters. Her abilities have been shown to be effective. Aikido is a fantastic defensive martial art. However lack of real world experience and lack of showing of her abilities make it difficult to put her in the running for best fighter. Perhaps she could become a contender with experience.
Makoto Kyogoku - Same as Ran likely. However, unlike Ran seems to keep a cooler head and not let his emotions get the better of him in life threatening situations. He is undefeated in the ring, and has been shown to be highly effective in real world situations, even taking a knife to his arm and not blinking, to defeat his opponent. However, lack of real world experience is a detriment. He is however in the running due to the aforementioned bout with a criminal. (Also being able to dodge a bullet (not possible, but still worth noting for the purposes of this comparison))
Subaru Okiya - Okiya is Akai, that is pretty apparent now. That means he took FBI hand to hand training. He was considered a top agent and likely had extensive experience all over the world and training in the FBI hand to hand combat techniques from the FBI training facility in Quantico. He is the a top contender for best fighter, due to this, despite not seeing anything first hand.
Masumi Sera - Jeet Kun Do practitioner. Now despite my own feelings about this "martial art" (I won't get into that now as it is irrelevant) it is probably the most effective of the chosen martial arts here. Mainly due to the philosophy of it, which is learn which is effective for you from various other martial arts, and take in what is most effective. Making a custom mixed martial art that accentuates the strengths of the practitioner and limits the weaknesses. Now naturally, if she learned the actual system that Bruce Lee devised, it is far less effective for her, mainly because it was designed for him, or whom he taught. There is only so much you can derive from that. If she took the essence of the system of which Bruce Lee devised it would make her a formidable foe. However, her lack of experience makes her hard to consider for "best." She is probably the best TEENAGED fighter of the bunch, just not overall.
Miwako Sato - Easily the best of the MPD. She has training, and by the looks of it has street fighting experience. While her technique is not perfectly refined, she knows an array of techinques and strikes and is physically strong. She has the experience to back it up as well. Being taught the police hand to hand combat techniques, and from what we have seen, she goes for grappling to subdue (standard police protocol) when possible. Of not she just goes crazy with striking. She has high levels of experience and high levels of training. She is an extremely strong contender.
Black Org Members - Well of the ones we have seen, it is likely that Gin, Bourbon and Vermouth are the most skilled in hand to hand. However, the amount of experience and skill they each have is completely unknown. Gin we know is tough as nails, shooting himself to not succumb to tranqs. Vermouth likely has training as an actress, and Bourbon likely as another top member who is active in the field also has experience. However, the lack of data makes it hard to come to any strict conclusion. It is possible that any of them could be stronger than anyone else.
SO! Overall... The teenagers are all out. Fighting a seasoned fighter would doom them. They couldn't keep up, and likely the more experienced knows what will work and be most effective from first hand experience. So Ran, Kazuha, Makoto and Sera are all not the strongest (Did anyone really expect them to be?)
Next is Kogorou... He has experience and training, but he is likely out of practice. That is the biggest detriment to him. If he was still active in the MPD he would likely be higher up there.
BO are simply too unknown. It is possible, but for the purposes of this, not going to happen. Gin is definitely tough, but does that make him the best fighter? Possible, but I can't say for certain. Vermouth probably has formal training. And Bourbon as well. As they are all close quarter and covert operatives. Meaning they would all need to know how to deal with close quarter combat. Lack of information prevents any significant conclusion though.
Then we finally come to Sato and Okiya. They are about the same in my book. I'd give the edge to Okiya due to rigor of training and international field work which would give him more experience. Also being trained in Quantico probably trumps the training facilities in Japan for the MPD.
So in my opinion Okiya is best fighter in Detective Conan